title: iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis.
abstract: A challenge in biodata analysis is to understand the underlying phenomena among many interactions in signaling pathways. Such study is formulated as the pathway enrichment analysis, which identifies relevant pathways functional enriched in high-throughput data. The question faced here is how to analyze different data types in a unified and integrative way by characterizing pathways that these data simultaneously reveal. To this end, we developed integrative Pathway Enrichment Analysis Platform, iPEAP, which handles transcriptomics, proteomics, metabolomics and GWAS data under a unified aggregation schema. iPEAP emphasizes on the ability to aggregate various pathway enrichment results generated in different high-throughput experiments, as well as the quantitative measurements of different ranking results, thus providing the first benchmark platform for integration, comparison and evaluation of multiple types of data and enrichment methods.
  
  
  METHODS
  iPEAP is freely available at http://www.tongji.edu.cn/∼qiliu/ipeap.html.
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Siping Rd. No. 1239, Shanghai 200092, Department of Computer Science, Hefei University of Technology, Tunxi Rd. No. 193, Hefei 230009, China and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA.
authors.forename: Haoqi
authors.initials: H
authors.lastname: Sun
authors.forename: Haiping
authors.initials: H
authors.lastname: Wang
authors.forename: Ruixin
authors.initials: R
authors.lastname: Zhu
authors.forename: Kailin
authors.initials: K
authors.lastname: Tang
authors.forename: Qin
authors.initials: Q
authors.lastname: Gong
authors.forename: Juan
authors.initials: J
authors.lastname: Cui
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Cao
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods*; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D055432:Metabolomics / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012984:Software